CorrelationHeatmap: Plot correlation heatmap

In CostaLab/scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference

Plot correlation heatmap

Description

This function will generate a combined heatmap with each one corresponding to the TF expression and binding activity as selected by using the function GetCorrelation. It was modified from the package ArchR. More details can be found: https://www.archrproject.com/bookdown/myeloid-trajectory-monocyte-differentiation.html

Usage

CorrelationHeatmap(
  trajectory1,
  trajectory2,
  name1 = NULL,
  name2 = NULL,
  labelRows1 = TRUE,
  labelRows2 = TRUE,
  labelTop1 = 50,
  labelTop2 = 50,
  limits1 = c(-2, 2),
  limits2 = c(-2, 2)
)

Arguments

trajectory1	A SummarizedExperiment object for TF activity generated by the function GetTrajectory
trajectory2	A SummarizedExperiment object for TF expression
name1	Name for the first object
name2	Name for the second object
labelRows1	Whether or not to show all labels for the first heatmap
labelRows2	Whether or not to show all labels for the second heatmap
labelTop1	A number indicating how many of the top N features, based on variance, should be labeled on the side of the first heatmap
labelTop2	A number indicating how many of the top N features, based on variance, should be labeled on the side of the second heatmap
limits1	A numeric vector of two numbers that represent the lower and upper limits of the second heatmap color scheme. generated by the function GetTrajectory
limits2	A numeric vector of two numbers that represent the lower and upper limits of the second heatmap color scheme. generated by the function GetTrajectory

Value

A heatmap

CostaLab/scMEGA documentation built on Sept. 25, 2024, 6:11 a.m.